Chuck vs the Memories and the Future
by theINTERSECT
Summary: What'll happen to Chuck and Sarah? Will she get her memories back? Or are they gone for good? My take on the continuation of Chuck vs the Bullet Train. A two chapter arc. A HAPPY ENDING IS GUARANTEED.
1. Chapter 1

**A/N: Hey guys. This is my take of what may happen to Chuck and Sarah (: It's a happy story...well maybe not the beginning, but it will be. I hope to finish it before the finale on Friday. It's sad to see Chuck go. It's been such a huge part of my life. I hope that the Chuck fandom will live on (: **

**Please forgive me if there are any mistakes, especially with the hospital/medical stuff...i'm not much of a medical/hospital-ish person (:**

**Disclaimer: I don't own Chuck.**

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><p>Sarah Walker woke up this morning with no recollection of the past 5 years of her life. She was no longer a Bartowski...no. It was not by will, but its just that she never knew anyone by the name Bartowski. Now if she'd never known a Bartowski, then how was she to know that she was a Bartowski.<p>

A man named Quinn came this morning and introduced himself to her as her handler. She had her doubts about him - he looked a little shady, and his facts were a little off, but who else was she to ask about what happened to her. She couldn't remember anything.

She'd learnt from a young age that in this line of business, you can never judge one by their cover. And so she didn't judge him. She accepted what he told her and made a note in her head to run a check on him the next chance possible.

He told her that she'd been knocked out for about a week. He asked her if she felt mentally and physically able to resume field work. She said 'yes'. A mission was a mission - she jumped at every chance she was given. She didn't care about the danger it brought; after all, it was a chance to escape from the realities of life. Her life was, well, she didn't really have a life. Her life was missions.

And so he gave her her next mission. Her next mission was to hunt down a guy by the name Chuck Bartowski, and kill him. He was the guy that was apparently responsible for her injuries.

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><p>She spent the day doing some preliminary research in preparation for the mission. Quinn had left her a computer with the CIA database downloaded onto it. She typed the name 'Chuck Bartowski' into the search engine and a load of information popped up. She clicked on the first result.<p>

Name: Charles (Chuck) Bartowski

Alias: Charles Carmicheal

Occpuation: Former CIA Agent, Owner of Carmicheal Industries and the Burbank Buymore

Family:

Wife: Sarah Bartowski nee Walker

Mother: Mary Bartowski

Father: Stephen (Orion) Bartowski

Sister: Ellie Bartowski - Woodcomb

Brother in Law: Devon Woodcomb

Niece: Clara Woodcomb

Notes: Former Intersect

Before she had the chance to read the contents of the page, she felt a churning sensation in her stomach. She rushed to the toilet, and regurgitated the contents of her breakfast into the toilet bowl. She hadn't had much for breakfast, so she was rather stunned at the amount of stuff that she could regurgitate.

She sat by the toilet bowl as she felt a second wave of throw up coming up. After purging the second time, she realized that she felt extremely weak, moody and emotional. It was strange. She'd never felt this way before. She was always one that could keep her emotions in check no matter what circumstance, and could stop herself from feeling emotions she didn't want to feel. She'd also never felt this way before after she threw up...it felt...different. The 'moody' side of her made her think something was wrong with her, and so she decided to get it checked out at a hospital.

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><p>She walked out of the toilet, supporting herself on various pieces of furniture as she went. She saw the computer on the desk on the far side of the room, but the 'tired' side of her was determined to walk as little as possible. She couldn't be bothered to walk that far. She eyed a cell phone on her dresser. She picked it up and searched up the nearest hospital. The first result that came up was Westside Hospital.<p>

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><p>Ellie had just finished her shift - she was on her way to her office to change and retrieve her stuff. She couldn't wait to get home to Clara.<p>

As she walked past the out-patient section, she thought she saw someone that resembled Sarah.

'Must be a coincidence.' She thought to herself. 'Must be my mind playing tricks on me because I miss her so much.'

'Ms Sarah Walker, this way please.'

Ellie turned back and saw Sarah.

She walked up to the nurse that was assisting Sarah, and told her that she'd take over from here.

'Sarah. Hey, how are you?' She asked.

'Good. Well, not really. I feel extremely tired, and I've thrown up a couple of times this morning...I never get sick.'

It was strange. Sarah was acting as if she didn't know her. And she'd just used her maiden name. She'd stopped using her maiden name (well Casey was an exception - he'd gotten used to calling her Walker.)

'Sarah, do you know who I am?'

Sarah was confused. Was she supposed to know who she was? She eyed the name tag on Ellie's shirt. 'Umm..Dr. Ellie Woodcomb?'

Ellie stared at her. She didn't mean to, but she couldn't help it.

'What? Am I supposed to know something?' Sarah asked. Her stomach started churning again. She felt stuff coming up. 'I..uhh...' She clasped her hand over her mouth. 'I need the toilet.'

Ellie swiftly led her into her office and into her toilet. They'd made it just in time. Sarah threw up into the toilet bowl.

When she was done, Ellie patted her back and handed her a cup of water. She then led Sarah out of the toilet and into her office.

'Here. Have a seat.' She told Sarah. She then proceeded to

'Ok. Let me check you. Open up.'

She carried out a serious of chekcs on Sarah. Nothing was wrong - she wasn't sick. Then it hit Ellie.

'Sarah, when did you last have your period?'

'Ummm...uhh...'

Ellie waited patiently as Sarah ransacked her mind.

After a while, she finally began talking. 'Umm...Dr Woodcomb, I honestly don't remember. I woke up this morning not remember anything.'

'Uhh...ok. Sarah, I'm going to need to carry out a couple more tests on you.'

Ellie paged a nurse, and got the nurse to bring her an ultrasound machine. After she'd completed the check, her suspicisions were confirmed.

'Sarah, uhh.. - '

ZZZZZ. Something was vibrating. It was her phone. She took it out of her pocket and saw that it was Chuck.

'Sorry..I need to take this. Wait here. I'll just be a minute.'

'Sure.' Sarah replied. Her mind was reeling. She saw the caller ID on the doctor's phone. It was Chuck Bartowski. _The mission._

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><p>Ellie stepped out of the room and answered the phone.<p>

'Hey Chuck. How are you holding up?'

'Uhh...not that well. I can only imagine how she felt when I was captured by the Belgian. But I'm trying.'

She heard the sound of a baby crying in the background.

'Sis, Clara won't stop crying. I thought you were supposed to be back ½ an hour ago. I think she's hungry.'

'Ohh...well..I'm a bit caught up here. I'll be back as soon as I can. Can you feed her for me? I've already prepared some milk in the fridge. Top shelf.'

'Uh...ok. Sure.'

There was a long pause. Ellie contemplated telling Chuck about Sarah.

'Found it. OK. See you later. Bye-' Chuck was about to hang up the phone.

'Chuck, wait.'

'Yea?'

'Chuck, ummm...uhh...' She hesitated. She didn't know whether she should tell him given the condition he was in. 'Uhhh...well...Sarah...Sarah's pregnant.'

'What? You mean...really? Wait..how do you know? Did you find her?'

'Chuck, I need you to calm down.'

'El, answer me.'

'Well..I was on my way to my office when I saw her.'

'Wait..she was at the hospital? Is she with you now? Are you still at the hospital?'

'Chuck, there's a thing...'

'El, are you guys still at the hospital?'

'Chuck. Listen.' She said sternly to get Chuck's attention. 'It seems that Sarah may have...well...I don't know how to put this...but she doesn't remember me. I think she may have lost her memories. She told me that she woke up this morning without any idea of anything that'd happened recently.'

There was a long silence. Ellie could tell that Chuck was thinking.

After a while, she decided to break the silence. 'Chuck?'

Chuck hesitated. 'El, did she mention anything about me?'

'Chuck...' He could tell by the tone in her voice that it meant no.

'El, is there a way to fix this?' There was a glitch in his voice.

'Maybe. I think I may have an idea, but I'm going to need some help. Look, I'm going to bring her to Castle. Call General Beckman. Meet me at Castle in 20. Bring Clara with you. I'll explain later.'

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><p><strong>AN: So what'ya guys think? Please drop me a review. It would be much appreciated. **

**Also, the next chapter of 'Chuck vs the Dads' is in the working. :)**


	2. Chapter 2

**A/N: Thanks to all who reviewed the first chapter. Here is the second chapter (: Hope you enjoy :P**

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><p>Ellie re-entered her office. Sarah was stood up, and she was pacing the room.<p>

'Sarah, I need you to come with me. I want to perform some additional tests on you.'

Sarah was, once again, confused. 'Why Doctor Woodcomb? Is there something you're not telling me? What's wrong with me?'

Ellie responded sternly. 'Sarah. I need you to come with me. Now. I'll explain later.' Without waiting for her response, Ellie took Sarah's wrist and started dragging her out to her car.

Sarah was dubious. She didn't know where she was taking her, but she seemed trustworthy enough. _I think. I hope. _She thought to herself.

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><p>When they entered Castle, Chuck was already sitting at the table, rocking Clara in his arms. General Beckman sat next to him, telling him about the idea Ellie had formulated as soon as Sarah'd downloaded the intersect.<p>

Ellie's theory was that if they found a way to completely remove the intersect like her dad had once acomplished with Chuck (before he downloaded the intersect 3.0), then her memories may return. This theory was based upon the fact that Morgan's intersect had only been suppressed. Because it had only been suppressed, it explains why his memories haven't returned.

Chuck looked up and saw Sarah and Ellie. Ellie took Clara out of Chuck's arms and began working with Beckman on her plan.

Chuck spent this time staring at Sarah.

'Sarah.' He was glad to see her, despite her condition.

'You are...' He seamed familiar, but she couldn't put her finger on it.

Chuck felt a pang in his heart. _She doesn't remember me_. He pulled himself together as he prepared to introduce himself to the love of his life.

'Chuck. I'm Chuck Bartowski.'

_The guy Quinn was talking about._ Sarah knew why she found him familiar - because Quinn had shown her a photo of him.

'Chuck Bartowski.' Sarah repeated. She took a moment to process all the information she had gathered in her head. 'Chuck Bartowski. You're the man I'm looking for.'

'You remember me?' Chuck felt hopeful.

'No. But my handler knows you. And he says that you're the person responsible for my injuries. You're the reason my last mission failed.' Sarah didn't know if what she was talking about was true, but she didn't care. Quinn was the first person that came to her, so she decided to go with his information.

Chuck felt his heart drop. He began zoning out. Sarah took advantage of this opportunity to deliver a blow to his head.

It came as a surprise to Chuck. When he recovered from the blow, he took a good look at Sarah. He looked straight into her crystal blue eyes. 'Sarah. I'm Chuck.'

'I know that.'

'Chuck, your husband. You are Sarah Bartowski.'

'There must have been a mistake. I'm Sarah Walker, not Bartowski.'

Chuck slipped his hand into his pocket and pulled out the picture they drew together on the train. 'Do you remember this?' He passed the picture to her.

'What? What is this?' She threw the picture onto the ground.

Chuck leaned over to pick it up. As he was getting up, Sarah delivered another blow to his stomach. Chuck fell to the ground, groaning. He knew he was going to get a couple of pretty nasty bruises, and maybe a few cuts. But he didn't care. He promised himself he wouldn't lift a single hair on Sarah's head.

'Sarah. Stop.'

'And why should I? Because you're scared? Because you're too weak to fight back?'

'Sarah...you can hit me all you want. You can kill me. But I'm not going to fight back.'

Sarah kicked him once more.

'Sarah...I love you.'

Sarah paused.

'What?'

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><p>Ellie and Beckman walked in just in time to witness this heart wrenching scene. Seeing the old Sarah was terrifying enough - seeing Sarah beat Chuck up was simply torture. They watched Sarah hit Chuck over and over again. Chuck wasn't doing anything to protect himself - his love for Sarah stopped him from doing so.<p>

'Sarah, stop. You're pregnant. You can't be fighting like that.'

'No. Not until he is dead. Quinn said so.' She filtered out the fact that she was pregnant. She was too focused on her task.

'Quinn?'

'He's my handler.'

'Are you sure'

'Yes. Well...I was going to run a background check on him this morning, but I totally forgot about it in midst of my sickness.'

'Well what if I told you now that he was a bad guy?'

'Well that doesn't matter, because I always finish my missions.'

She threw him against a wall. Chuck was holding up rather well, considering the situation he was in.

'AGENT WALKER.' Beckman said sternly. Sarah paused again. Ellie and Beckman took this opportunity to bind Sarah's hands together and drag her away from Chuck.

They led her into a cell, where Ellie's intersect removal system was set up. They sat Sarah on a chair. Ellie activated the system, and both her and Beckman promptly left the room.

Ellie ran towards Chuck, and helped him up.

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><p>Chuck spent the whole time waiting outside the cell door, despite his weak condition. Ellie tried to coax him into a chair, but he refused. He was extremely worried. <em>What if it doesn't work?<em> He thought to himself. He hoped that it would.

After the sequence was over, Sarah passed out. Chuck immediately forced the door open with his remaining strength, picked her up, and set her down on the cot in the cell. He collapsed on the floor after doing so.

Ellie helped him into a chair, and began to treat his injuries. She tried to convince him to leave the room, but he once again refused. He wanted to stay by Sarah. Ellie warned him that she could be hostile towards him if the intersect removal system didn't work. He didn't care.

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><p>20 minutes later, Sarah regained consciousness, but remained quiet.<p>

Ellie was still bandaging Chuck up. Chuck had his head down, and Ellie was focused on tending to Chuck's wounds.

Sarah lay awake for a while, staring at the ceiling, remembering everything, processing everything. The intersect removal system had worked.

She remembered the conversations she and Chuck had on the train, the things that they did, and the picture they drew.

She remembered being captured by Quinn and she remembered him surpressing her memories.

She remembered waking up not knowing anything.

She remembered going to the hospital, but getting no conclusion of the cause of her sickness.

And finally, she remembered being given the mission to kill Chuck, and she was stupid enough to somewhat follow through.

'AHH. Sis, that hurts.' Sarah turned her head sideways to track where the sound came from. She saw Chuck sitting in a chair next to her cot, with Ellie trying to clean his cuts. Chuck held an ice pack to his forehead. Apparently, she'd beaten him up pretty bad.

'She told me she would never forget this. Our future.' She spotted the picture they'd drawn together on the train. 'She promised me.'

She hated herself for putting him through such an ordeal. She hated herself for beating him up. She hated seeing him like this. She promised herself she'd make up for it. She knew she'd hurt him bad, both emotionally and physically.

'Chuck.' She whispered.

They didn't hear her.

'Chuck.' She said louder.

Chuck and Ellie both turned their heads to her. Chuck dropped everything, stood up, and moved to sit on the edge of the cot, almost stumbling on the way. Ellie was reluctant to let him get so close to Sarah, because she didn't know whether the system had worked. She also hadn't finished cleaning Chuck's cuts. But she had no choice. She knew Chuck wouldn't listen. She proceeded to pick up everything Chuck had dropped and placed the items on the chair.

'Sarah.' He breathed. He put his hand on her cheek, hoping she'd recovered.

Sarah slowly sat up. She placed her hands on top of Chuck's.

'Chuck, I'm sorry.' A tear rolled sown her face.

Chuck used the palm of his thumb to wipe the stray tear away. 'Don't be.'

'No, Chuck, I did this...'. She ran her finger across a bruise that'd formed on his arm and motioned to the rest of the cuts and bruises he had. 'I remember.'

'You remember?'

'Yes. Quinn made me. He manipulated me. And I was stupid enough to trust him.'

He pulled his hands out from under Sarah's and took both her hands in his. 'It doesn't matter Sarah. All that matters is that you remember.'

'I remember Chuck, I remember. I'm Sarah Bartowski. And you're my husband.'

She saw the picture on the chair.

'And I remember this as well.' She picked up the picture. 'Our future. The picket fenced house. The baby...or even babies.' She chuckled quietly. 'Someday.' She paused. 'I remember, Chuck, I remember.'

Chuck brought his lips to Sarah's, and they kissed. The kiss was beginning to heat up when Chuck let out a cry of pain.

'OW.' They broke the kiss.

'Chuck, your head is bleeding.' Sarah began search for something that'd be able to stop the bleeing. Ellie came to the rescue with a white cloth. She pressed it to Chuck's head.

'Elie, let me.' Ellie let Sarah take over.

Ellie suddenly remembered that Sarah didn't know that she was pregnant. 'Chuck, she doesn't know.'

'Know about what?' Chuck replied, clearly confused.

'The thing I told you earlier...you know...'

Chuck suddenly understood. 'Ok.'

Sarah cut in. 'What's going on here? Did I miss something when I was gone? Chuck, is there something you'd like to tell me?'

'UHH...' Chuck smiled. He looked at Ellie.

Ellie felt that she was intruding in on their private time. 'Sarah, let me bandage Chuck up here and I'll leave you two to it.'

'OK.' Sarah reluctantly lets go of Chuck, but makes faces at him.

Chuck tries to hold his laughter in as Ellie finishes up on him. When Ellie finishes, she leaves the room with a smile on her face.

Chuck settled himself next to Sarah on the cot. It was a tight fit, but it was perfect. Chuck draped his good arm around Sarah's shoulders. Sarah leaned on Chuck's chest, being careful hurt any of his injuries.

'So, what? What don't I know?' Sarah looked up at Chuck.

Chuck was still thinking of the best way to tell her. 'OK. Don't freak out.'

'I won't. I promise. Having been a spy for so long, I've had my share of surprises. I promise I won't freak out.'

'OK.' He paused and smiled. 'Soo...So remember how you went to the hospital...'

'Just tell me.' Sarah whined happily.

'OK. Uhh...we're going to be parents.'

Chuck said it so quickly that Sarah didn't didn't have time to process it.

'Hmmm...ok.' It took her a couple of seconds understand what Chuck had just told her. Chuck found it amusing watching her do so.

'Wait..does that mean I'm - '

'Pregnant.' They said in unison.

Chuck placed his hand on Sarah's stomach. 'We're having a baby.' Huge smiles broke out on both of their faces.

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><p><strong>AN: THE ENDDD. ****Told you there'd be a happy ending. (: One more day till Chuck is officially over...its gonna be the saddest day ever. :(**

****I'm considering an epilogue...maybe..possibly...(: **Please review :P**


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